Wetlands rank among the worlds most imperiled ecosystems with the highest rates of habitat destruction, degradation, and loss of biodiversity. This is especially true for ephemeral vernal pool wetlands found in the Great Central Valley of California, USA, a region impacted by urbanization and high agricultural productivity. Vernal pools are island-like temporary wetlands that form during rainy winter months, dry completely in the summer months and are often found in Mediterranean climates around the world – including in Western Australia! Environmental DNA (eDNA) metabarcoding is increasingly used to catalogue and assess biodiversity and offers a promising, modern approach to biomonitoring. Yet, many methodological and technical challenges remain (e.g. sample processing, marker selection, concordance, etc). Vernal pools serve as ideal testing grounds to understand both species detection using eDNA and how biological communities may shift across time, space, and environmental heterogeneity. Vernal pools represent areas of high native plant diversity and endemism, but due to habitat destruction and fragmentation many species are threatened and there is an urgent need to monitor their biodiversity. However, traditional species surveys require time and taxonomic expertise, and are complicated by dormancy or the phenological stages of species at the time surveys are taken. We conducted an eDNA metabarcoding experiment of the soil seed bank of vernal pools in the Great Central Valley using three marker regions (trnL, ITS2 and rbcL) and compared soil eDNA methodologies to traditional plant surveys in the field and in a seed bank emergence trial. We found strong concordance between eDNA and traditional survey techniques and detected an endangered plant species, Colusa grass (Neostapfia colusana) in a site it is known to occur. Lastly, we discuss our current work on sample optimization and processing methodologies to improve the capacity of eDNA to aid biomonitoring efforts within temporary, or otherwise challenging ecosystems.